Enzyme function initiative-enzyme similarity tool (EFI-EST): a web tool for generating protein sequence similarity networks

JA Gerlt, JT Bouvier, DB Davidson, HJ Imker… - … Et Biophysica Acta (BBA …, 2015 - Elsevier
Abstract The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale
Collaborative Project (EFI; U54GM093342; http://enzymefunction. org/), is focused on …

Genomic enzymology: web tools for leveraging protein family sequence–function space and genome context to discover novel functions

JA Gerlt - Biochemistry, 2017 - ACS Publications
The exponentially increasing number of protein and nucleic acid sequences provides
opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural …

Cultivation of marine bacteria of the SAR202 clade

Y Lim, JH Seo, SJ Giovannoni, I Kang… - Nature …, 2023 - nature.com
Bacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed
in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient …

A homoeostatic switch causing glycerol-3-phosphate and phosphoethanolamine accumulation triggers senescence by rewiring lipid metabolism

K Tighanimine, JA Nabuco Leva Ferreira Freitas… - Nature …, 2024 - nature.com
Cellular senescence affects many physiological and pathological processes and is
characterized by durable cell cycle arrest, an inflammatory secretory phenotype and …

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes

MW Vetting, N Al-Obaidi, S Zhao, B San Francisco… - Biochemistry, 2015 - ACS Publications
The rate at which genome sequencing data is accruing demands enhanced methods for
functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the …

The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to …

I Kang, S Kim, MR Islam, JC Cho - Scientific reports, 2017 - nature.com
The acI lineage of the phylum Actinobacteria is the most abundant bacterial group in most
freshwater lakes. However, due to difficulties in laboratory cultivation, only two mixed …

Exploring d-xylose oxidation in Saccharomyces cerevisiae through the Weimberg pathway

L Wasserstrom, D Portugal-Nunes, H Almqvist… - AMB Express, 2018 - Springer
Engineering of the yeast Saccharomyces cerevisiae towards efficient d-xylose assimilation
has been a major focus over the last decades since d-xylose is the second most abundant …

Prediction of enzymatic pathways by integrative pathway mapping

S Calhoun, M Korczynska, DJ Wichelecki… - Elife, 2018 - elifesciences.org
The functions of most proteins are yet to be determined. The function of an enzyme is often
defined by its interacting partners, including its substrate and product, and its role in larger …

[HTML][HTML] Diversity in protein domain superfamilies

S Das, NL Dawson, CA Orengo - Current opinion in genetics & …, 2015 - Elsevier
Whilst∼ 93% of domain superfamilies appear to be relatively structurally and functionally
conserved based on the available data from the CATH-Gene3D domain classification …

Characterization and mutagenesis of two novel iron–sulphur cluster pentonate dehydratases

M Andberg, N Aro-Kärkkäinen, P Carlson, M Oja… - Applied microbiology …, 2016 - Springer
We describe here the identification and characterization of two novel enzymes belonging to
the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc …